Contacts of the helix formed by residues 13 - 36 (chain C) in PDB entry 6XWQ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 13 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ASP 3.5 4.0 - - - +
12C TYR* 1.3 100.3 - - + +
14C VAL* 1.3 56.7 + - - +
15C LEU* 3.1 3.3 + - + +
16C TRP* 3.7 31.6 - - + +
17C LYS* 2.8 35.2 + - - +
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Residues in contact with VAL 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C TYR 3.3 5.3 + - - +
13C PRO* 1.3 71.6 - - - +
15C LEU* 1.3 65.3 + - + +
17C LYS* 4.0 11.2 - - - +
18C ILE* 3.2 25.8 + - + +
204C MET* 3.4 44.0 - - + +
205C GLN* 4.1 17.7 - - + +
273C THR* 5.2 0.6 + - - -
286C VAL* 5.8 8.5 - - + -
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Residues in contact with LEU 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C PRO* 3.1 3.7 - - + +
14C VAL* 1.3 82.6 - - + +
16C TRP* 1.3 74.5 + - + +
18C ILE* 3.1 19.8 - - + +
19C LEU* 3.4 8.8 + - + +
268C LYS* 5.7 0.7 - - - +
269C ASP* 3.9 39.5 - - + +
272C ILE* 3.9 31.9 - - + -
273C THR* 3.8 21.3 - - - +
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Residues in contact with TRP 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C TYR* 4.8 8.7 - - + +
13C PRO* 3.3 27.2 + - + +
15C LEU* 1.3 85.8 - - + +
17C LYS* 1.3 60.1 + - - +
19C LEU* 3.3 28.7 + - + -
20C TRP* 2.8 43.6 + + - +
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Residues in contact with LYS 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C TYR* 3.2 47.3 + - + +
10C LEU 4.8 1.8 - - - -
12C TYR* 3.6 36.7 - - + -
13C PRO 2.8 19.8 + - - +
14C VAL* 4.3 6.8 - - - +
16C TRP* 1.3 72.8 - - - +
18C ILE* 1.3 57.5 + - - +
20C TRP* 3.0 10.8 + - + +
21C GLY* 2.8 28.2 + - - -
204C MET 4.6 0.4 + - - -
205C GLN* 3.1 34.9 + - - +
208C PRO* 3.2 26.5 - - + +
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Residues in contact with ILE 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C VAL* 3.2 18.5 + - + +
15C LEU* 3.1 24.7 - - + +
17C LYS* 1.3 77.5 - - - +
19C LEU* 1.3 59.6 + - + +
21C GLY* 4.1 0.6 - - - -
22C LEU 3.6 8.8 + - - -
204C MET* 5.8 2.2 - - - -
207C ALA* 3.4 48.2 - - + +
208C PRO* 3.4 10.9 - - + +
211C VAL* 3.7 13.1 - - + +
272C ILE* 5.3 0.4 - - + -
273C THR* 4.3 20.2 - - + +
276C VAL* 3.1 44.8 - - + +
277C THR* 5.0 7.2 - - - +
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Residues in contact with LEU 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C LEU* 3.4 9.6 + - + +
16C TRP* 3.3 35.1 + - + +
17C LYS 3.1 0.6 - - - -
18C ILE* 1.3 80.6 - - - +
20C TRP* 1.3 59.2 + - - +
21C GLY 3.3 0.2 - - - -
22C LEU* 3.3 10.9 + - + +
23C VAL* 2.9 32.1 + - + +
272C ILE* 3.8 29.2 - - + -
275C PHE* 5.9 2.2 - - + -
276C VAL* 3.7 23.1 - - + -
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Residues in contact with TRP 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C TYR* 5.2 16.6 - + + -
16C TRP* 2.8 31.9 + + + +
17C LYS* 3.0 11.6 + - + +
19C LEU* 1.3 77.8 - - - +
21C GLY* 1.3 59.0 + - - +
23C VAL* 3.2 21.3 - - + +
24C LEU* 3.0 57.5 + - + +
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Residues in contact with GLY 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C LYS 2.8 14.6 + - - -
18C ILE 4.5 1.3 - - - -
20C TRP* 1.3 80.9 - - - +
22C LEU* 1.3 56.1 + - - +
24C LEU* 3.4 5.0 + - - +
25C GLY* 2.9 26.2 + - - -
208C PRO* 4.3 18.8 - - - +
211C VAL* 4.4 5.8 - - - -
212C PHE* 4.0 13.9 - - - +
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Residues in contact with LEU 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ILE 3.6 17.4 + - - +
19C LEU* 3.3 12.7 + - + +
20C TRP 3.3 0.4 - - - -
21C GLY* 1.3 76.2 - - - +
23C VAL* 1.3 60.8 + - - +
24C LEU 3.5 0.3 + - - -
25C GLY* 3.6 7.3 + - - +
26C ALA* 3.6 13.2 + - - +
211C VAL* 3.8 16.9 - - + +
215C ILE* 3.7 33.0 - - + -
275C PHE* 4.4 10.1 - - + -
276C VAL* 3.6 26.9 - - + -
399C MET* 3.8 29.4 - - + -
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Residues in contact with VAL 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 2.9 18.9 + - + +
20C TRP* 3.2 36.8 - - + +
22C LEU* 1.3 77.0 - - - +
24C LEU* 1.3 63.7 + - + +
26C ALA* 4.3 5.1 + - + +
27C VAL* 3.9 19.2 + - - +
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Residues in contact with LEU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C TRP* 3.0 51.2 + - + +
21C GLY* 3.9 4.9 - - - +
23C VAL* 1.3 82.1 - - + +
25C GLY* 1.3 58.0 + - - +
26C ALA 3.3 2.5 - - - -
27C VAL* 3.3 15.7 + - + +
28C PHE* 3.0 28.8 + - - +
212C PHE* 3.8 13.6 - - + -
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Residues in contact with GLY 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C GLY 2.9 14.3 + - - -
22C LEU 3.6 0.8 + - - -
23C VAL 3.5 0.4 - - - -
24C LEU* 1.3 78.1 - - - +
26C ALA* 1.3 55.4 + - - +
29C GLY* 2.9 25.6 + - - -
212C PHE* 3.5 20.3 - - - -
215C ILE* 3.7 20.4 - - - +
216C ALA* 3.5 13.6 - - - +
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Residues in contact with ALA 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LEU 3.6 13.5 + - - +
23C VAL* 4.5 7.0 - - + +
24C LEU 3.3 0.6 - - - -
25C GLY* 1.3 76.2 - - - +
27C VAL* 1.3 65.0 + - + +
29C GLY* 3.4 0.5 + - - -
30C LEU* 2.9 33.2 + - + +
215C ILE* 4.2 5.1 - - + +
219C MET* 4.0 20.6 - - + -
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Residues in contact with VAL 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C VAL 3.9 14.4 - - - +
24C LEU* 3.3 19.6 + - + +
26C ALA* 1.3 77.8 - - + +
28C PHE* 1.3 59.4 + - - +
30C LEU* 3.3 8.3 + - - +
31C ILE* 2.9 31.7 + - + +
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Residues in contact with PHE 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C LEU 3.0 8.4 + - - +
25C GLY 4.0 0.7 - - - +
27C VAL* 1.3 75.9 - - - +
29C GLY* 1.3 59.6 + - - +
31C ILE* 3.1 22.0 - - + +
32C ALA* 2.9 30.6 + - + +
41C VAL* 3.7 22.2 - - + -
45C ILE* 3.4 34.8 - - + -
212C PHE* 3.6 35.4 - + + -
216C ALA* 3.5 26.0 - - + -
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Residues in contact with GLY 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C GLY 2.9 15.1 + - - -
28C PHE* 1.3 78.8 - - - +
30C LEU* 1.3 58.3 + - - +
32C ALA* 3.3 1.0 + - - +
33C GLY* 2.9 24.3 + - - -
216C ALA* 3.6 24.5 - - - -
219C MET* 3.7 10.3 - - - -
220C ALA* 3.4 18.3 - - - -
223C GLY* 5.9 0.5 - - - -
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Residues in contact with LEU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ALA* 2.9 28.7 + - + +
27C VAL* 3.6 7.6 - - - +
29C GLY* 1.3 75.5 - - - +
31C ILE* 1.3 59.5 + - - +
33C GLY* 3.4 2.4 + - - +
34C HIS* 2.9 26.9 + - - +
219C MET* 3.7 25.8 - - + -
223C GLY* 5.6 9.2 - - - +
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Residues in contact with ILE 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C VAL* 2.9 15.7 + - + +
28C PHE* 3.1 39.5 - - + +
30C LEU* 1.3 76.3 - - - +
32C ALA* 1.3 58.0 + - - +
34C HIS* 3.3 17.4 + - + +
35C PHE* 2.9 42.5 + - + +
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Residues in contact with ALA 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C PHE* 2.9 22.8 + - + +
29C GLY* 3.6 5.2 - - - +
31C ILE* 1.3 76.2 - - + +
33C GLY* 1.3 53.9 + - - +
35C PHE* 3.0 8.1 + - - +
36C GLY 2.7 31.9 + - - -
37C TYR* 3.3 15.3 + - + +
38C ALA 5.2 0.9 - - - -
41C VAL* 4.2 21.1 - - + -
220C ALA* 3.7 18.2 - - + -
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Residues in contact with GLY 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C GLY 2.9 15.0 + - - -
30C LEU* 3.7 3.6 - - - -
32C ALA* 1.3 76.3 - - - +
34C HIS* 1.3 60.6 + - - +
36C GLY* 3.3 12.7 + - - -
38C ALA* 5.8 1.3 - - - -
220C ALA* 4.3 15.5 - - - +
223C GLY* 6.0 4.7 - - - -
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Residues in contact with HIS 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU 2.9 14.7 + - - +
31C ILE* 3.3 21.3 + - + +
32C ALA 3.1 0.2 - - - -
33C GLY* 1.3 77.6 - - - +
35C PHE* 1.3 102.9 + + - +
36C GLY* 3.0 2.2 + - - -
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Residues in contact with PHE 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ILE* 2.9 29.6 + - + +
32C ALA* 3.0 9.6 + - - +
34C HIS* 1.3 104.7 + + - +
36C GLY* 1.3 61.3 + - - +
37C TYR* 3.2 33.0 - + + +
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Residues in contact with GLY 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ALA 2.7 12.9 + - - -
33C GLY* 3.3 10.7 + - - -
34C HIS 3.0 5.6 - - - -
35C PHE* 1.3 75.5 - - - +
37C TYR* 1.3 56.9 + - - -
38C ALA* 3.4 8.2 + - - -
39C GLY 5.3 0.2 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il